NAMD - A PARALLEL, OBJECT-ORIENTED MOLECULAR-DYNAMICS PROGRAM

NAMD is a molecular dynamics program designed for high performance sim ulations of large biomolecular systems on parallel computers. An objec t-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition co upled with a multithreaded, message-driven design, which is shown to s cale efficiently to multiple processors. Also, NAMD incorporates the d istributed parallel multipole tree algorithm for full electrostatic fo rce evaluation in O(N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interac tive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illustr ates the performance of NAMD.